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Data from: Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

Seeb LW, Templin WD, Sato S, Abe S, Warheit K, Park JY, Seeb JE

Date Published: March 16, 2011

DOI: http://dx.doi.org/10.5061/dryad.8849

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Title

PacSNP chum data for MER

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Description

The file is formatted for GenAlEx software, but can easily be converted to Genepop or similar formats. Genotypes are in two-column format with missing data designated with a “0”. Population code and locus code worksheets follow the rawdata. The population order differs between the rawdata which is in numeric order and Table 1 of the manuscript which is ordered geographically. This is particularly noticeable in the order of the Western Alaska populations including the Yukon River. The rawdata includes laboratory names for the SNPs; a key to published names is in the locus code worksheet. The mtDNA SNPs are listed independently and have not been combined into composite haplotypes.

AbstractStudies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometers, have become increasingly valuable in the presence of climate change, increasing hatchery production, and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive datasets from spawning populations originating from across the species? range. Single nucleotide polymorphisms (SNPs) have been particularly amenable for multi-national applications because they are easily shared, require little inter-laboratory standardization, and can be assayed through increasingly efficient technologies. Here we discuss the development of a dataset for 114 populations of chum salmon through a collaboration among North American and Asian researchers, termed PacSNP. PacSNP is focused on developing the database and applying it to problems of international interest. A dataset spanning the entire range of species provides a unique opportunity to examine patterns of variability, and we review issues associated with SNP development. We found evidence of ascertainment bias within the dataset, variable linkage relationships between SNPs associated with ancestral groupings, and outlier loci with alleles associated with latitude.